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Update package/MDAnalysis/analysis/msd.py
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package/MDAnalysis/analysis/msd.py

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:class:`~MDAnalysis.transformations.nojump.NoJump`
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transformation to unwrap coordinates on-the-fly.
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A minimal example:
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.. code-block:: python
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import MDAnalysis as mda
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from MDAnalysis.transformations import NoJump
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u = mda.Universe(TOP, TRAJ)
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# Apply NoJump transformation to unwrap coordinates
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u.trajectory.add_transformations(NoJump(u))
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# Now the trajectory is unwrapped and MSD can be computed normally:
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from MDAnalysis.analysis.msd import EinsteinMSD
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MSD = EinsteinMSD(u, select="all", msd_type="xyz")
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MSD.run()
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A minimal example:
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.. code-block:: python
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import MDAnalysis as mda
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from MDAnalysis.transformations import NoJump
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u = mda.Universe(TOP, TRAJ)
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# Apply NoJump transformation to unwrap coordinates
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u.trajectory.add_transformations(NoJump(u))
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# Now the trajectory is unwrapped and MSD can be computed normally:
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from MDAnalysis.analysis.msd import EinsteinMSD
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MSD = EinsteinMSD(u, select="all", msd_type="xyz")
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MSD.run()
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This example assumes that the trajectory contains periodic box
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dimensions. If no periodic boundary information is present, box
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dimensions must be defined before applying ``NoJump``, which can

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